Ab Initio Molecular Orbital Calculations of DNA Radical Ions. 5. Scaling of Calculated Electron Affinities and Ionization Potentials to Experimental Values

Sevilla, Michael D.; Besler, Brent; Colson, Anny‐Odile

doi:10.1021/j100003a032

Cited by 219 publications

(233 citation statements)

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“…Using different theoretical methods, the gas-phase ionization potential of DNA bases were also calculated. [34][35][36][37][38][39][40][41] A comparison of the theoretically calculated IP values of G, A, C and T along with their corresponding experimental values are presented in Table 1.1. In Table 1.1, we see that both theory and experiment predict the same order of ionization potential of DNA bases as G < A < C < T.…”

Section: Ionization Potential Of Dna Bases and Base Pairsmentioning

confidence: 99%

Theoretical Modeling of Radiation‐Induced DNA Damage

Kumar

Sevilla

2009

Radical and Radical Ion Reactivity in Nucleic Acid Chemistry

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Section: Ionization Potential Of Dna Bases and Base Pairsmentioning

confidence: 99%

Theoretical Modeling of Radiation‐Induced DNA Damage

Kumar

Sevilla

2009

Radical and Radical Ion Reactivity in Nucleic Acid Chemistry

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“…The orbital overlapping and the distribution of the HOMOs over the oligomer structure directly influence the charge distribution in the DNA molecule and the inner- [22] b Experimental data [22,26,27] sphere reorganization energy, respectively. We have calculated the inner-sphere reorganization energy and the vIP for the separated nucleobases and their pairs.…”

Section: B Inner-sphere Reorganization Energymentioning

confidence: 99%

“…From Table II it is clear that our calculation and the experimental results for the nucleobases are in good agreement except for cytosine. Unfortunately, the experimental values were defined as the difference between the vertical ionization potential and the adiabatic ionization potential, with values extracted from different sources [22,26,27]. As a result, in general the final values can be inaccurate due to the use of different experimental techniques and agreement of the theoretical data with the experiment is not completely reliable.…”

Section: B Inner-sphere Reorganization Energymentioning

confidence: 99%

Energetics of the hole transfer in DNA duplex oligomers

Berashevich

Chakraborty

2007

Chemical Physics Letters

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We report on our calculations of the inner-sphere reorganization energy and the interaction of the π orbitals within DNA oligomers. The exponential decrease of the electronic coupling between the highest and second highest occupied base orbitals of the intrastrand nucleobases in the (A-T)n and (G-C)n oligomers have been found with an increase of the sequence number n in the DNA structure. We conclude that for realistic estimation of the electronic coupling values between the nucleobases within the DNA molecule, a DNA chain containing at least four base pairs is required. We estimate the geometry relaxation of the base pairs within the (A-T)n and (G-C)n oligomers (n = 1 − 6) due to their oxidation. The decrease of the inner-sphere reorganization energy with elongation of the oligomer structure participating in the oxidation process have been observed. The maximum degree of geometry relaxation of the nucleobase structures and correspondingly the higher charge density in the oxidized state are found to be located close to the oligomer center.

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“…The corresponding anion is the lowest energy of the 10 studied here. That the radical with the lowest AEA results from H-abstraction from cytosine is not surprising, because cytosine has been shown to have a higher AEA than guanine and to function as something of a sink for negative charge (29,30).…”

Section: Table 5 H-bond Distances Of the Deprotonated G-c Structuresmentioning

confidence: 99%

The deprotonated guanine-cytosine base pair

Lind

Bera

Richardson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Awareness of the harmful effects of radiation has increased interEnergetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine-cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal⅐mol ؊1 , vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal⅐mol ؊1 lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H⅐⅐⅐O2 distance dramatically reduced from 1.88 to 1.58 Å, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a "reverse wobble" incorporating two N-H⅐⅐⅐N hydrogen bonds. Three different types of relaxation energies (4.3-54 kcal⅐mol ؊1 ) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.electron affinities ͉ nucleic acid bases ͉ radiation damage ͉ strand breaks L esions in DNA caused by both high-and low-energy electrons are thought to result in cancer cell formation. Consequently, the mechanisms of primary and secondary damage to purinepyrimidine base pairs have been under intense investigation in recent years (1-15). Radical and anion formation in DNA are thought to be steps in pathways arising from radiation damage, which can lead to mutations (15). This mutation can happen in several different ways, including direct radiation damage, secondary ballistic electron damage, or chemical damage by oxidative species (15). Additionally, electronic properties of DNA have been under scrutiny with the hopes of using DNA strands in molecular electronic devices (16)(17)(18).Illenberger and coworkers (3, 4) have noted, based on electron͞nucleobase collision experiments, that dehydrogenation of bases is the predominant dissociative channel for DNA. Highenergy photons, for example in the form of UV radiation from the sun, release electrons, which, in turn, may induce alterations such as single-and double-strand breaks in DNA or deletions of entire segments of the strand (19). This process can occur through a number of pathways, one of which is dissociative electron attachment (DEA), whereby electrons formed as secondary products of radiation bind to nucleobases and cause bonds to break. have shown that DEA yields bases that are dehydrogenated predominantly at nitrogen sites. Furthermore, their work notes that the N-H bond that is cleaved in the isolated ...

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Ab Initio Molecular Orbital Calculations of DNA Radical Ions. 5. Scaling of Calculated Electron Affinities and Ionization Potentials to Experimental Values

Cited by 219 publications

References 4 publications

Theoretical Modeling of Radiation‐Induced DNA Damage

Theoretical Modeling of Radiation‐Induced DNA Damage

Energetics of the hole transfer in DNA duplex oligomers

The deprotonated guanine-cytosine base pair

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